PCDHA5

protocadherin alpha 5, the group of Clustered protocadherins

Basic information

Region (hg38): 5:140821603-141012347

Previous symbols: [ "CNRS6" ]

Links

ENSG00000204965 ∙ NCBI:56143 ∙ OMIM:606311 ∙ HGNC:8671 ∙ Uniprot:Q9Y5H7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCDHA5 gene.

• Inborn genetic diseases (470 variants)
• not provided (57 variants)
• not specified (1 variants)
• Thrombocytosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCDHA5 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			40	6		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			401	78	1	480
Total	0	0	441	87	1

Variants in PCDHA5

This is a list of pathogenic ClinVar variants found in the PCDHA5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-140821788-C-T		not specified	Uncertain significance (Dec 12, 2023)
5-140821879-C-G		not specified	Uncertain significance (Dec 21, 2022)
5-140821897-G-C		not specified	Uncertain significance (Apr 25, 2022)
5-140821900-C-A		not specified	Uncertain significance (Jan 31, 2023)
5-140821900-C-G		not specified	Uncertain significance (Aug 15, 2023)
5-140821968-G-A		not specified	Uncertain significance (Apr 07, 2023)
5-140821983-C-G		not specified	Uncertain significance (Apr 07, 2023)
5-140822041-T-G		not specified	Uncertain significance (Dec 12, 2023)
5-140822061-C-G		not specified	Likely benign (Apr 07, 2023)
5-140822067-A-T		not specified	Uncertain significance (Dec 06, 2022)
5-140822110-C-T		not specified	Uncertain significance (Apr 05, 2023)
5-140822192-A-C		not specified	Uncertain significance (Jan 12, 2024)
5-140822281-A-G		not specified	Uncertain significance (Jul 14, 2023)
5-140822373-G-A		not specified	Uncertain significance (May 31, 2022)
5-140822613-T-C		not specified	Uncertain significance (Nov 17, 2023)
5-140822628-C-T		not specified	Uncertain significance (Jan 23, 2023)
5-140822737-C-T		not specified	Uncertain significance (Jul 14, 2021)
5-140822752-C-A		not specified	Uncertain significance (Apr 14, 2022)
5-140822757-C-G		not specified	Uncertain significance (Jul 13, 2022)
5-140822821-T-C		not specified	Uncertain significance (Feb 28, 2024)
5-140822853-G-A		not specified	Uncertain significance (Jul 20, 2021)
5-140822890-G-C		not specified	Likely benign (Sep 14, 2022)
5-140822955-T-G		not specified	Uncertain significance (Jun 06, 2023)
5-140822994-G-A		not specified	Uncertain significance (Aug 13, 2021)
5-140823028-C-T		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCDHA5	protein_coding	protein_coding	ENST00000529859	4	190708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.84e-8	0.966	125581	1	166	125748	0.000664

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.414	606	578	1.05	0.0000416	6015
Missense in Polyphen		164	157.72	1.0398		1887
Synonymous	-0.781	296	279	1.06	0.0000242	2029
Loss of Function	2.05	16	27.7	0.579	0.00000141	339

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00234	0.00227
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.00109	0.00109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000442	0.000431
Middle Eastern	0.00109	0.00109
South Asian	0.000654	0.000621
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Intolerance Scores

• loftool: 0.804
• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.76

Haploinsufficiency Scores

• pHI: 0.0984
• hipred: N
• hipred_score: 0.439

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0567

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pcdha5

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;nervous system development
• Cellular component: integral component of plasma membrane
• Molecular function: calcium ion binding